Explore Workflows
View already parsed workflows here or click here to add your own
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count-lines13-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c |
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Build Bowtie indices
Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome |
https://github.com/datirium/workflows.git
Path: workflows/bowtie-index.cwl Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e |
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steplevel-resreq.cwl
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https://github.com/common-workflow-language/common-workflow-language.git
Path: v1.0/v1.0/steplevel-resreq.cwl Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2 |
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RNA-Seq pipeline paired-end strand specific
The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file |
https://github.com/datirium/workflows.git
Path: workflows/rnaseq-pe-dutp.cwl Branch/Commit ID: 282762f8bbaea57dd488115745ef798e128bade1 |
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heatmap.cwl
Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension |
https://github.com/datirium/workflows.git
Path: workflows/heatmap.cwl Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf |
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mutect parallel workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/mutect.cwl Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca |
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gathered exome alignment and somatic variant detection for cle purpose
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_exome_cle_gathered.cwl Branch/Commit ID: 42c66dd24ce5026d3f717214ddb18b7b4fae93cf |
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pair-workflow.cwl
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https://github.com/mskcc/argos-cwl.git
Path: workflows/pair-workflow.cwl Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6 |
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search.cwl#main
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/search.cwl Branch/Commit ID: 5c7799a145595323d0a8628be1fe0e24985e793a Packed ID: main |
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scatter-wf2_v1_1.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/scatter-wf2_v1_1.cwl Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0 |
